Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2561
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 46077
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Found at i:3516 original size:2 final size:2
Alignment explanation
Indices: 3509--3535 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3499 CCTCCTGAGA
3509 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3536 ATGTTTTGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3887 original size:2 final size:2
Alignment explanation
Indices: 3880--3914 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3870 TAGAAATTGA
*
3880 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3915 AACATTGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6156 original size:11 final size:11
Alignment explanation
Indices: 6140--6165 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6130 TATAAATTTT
6140 AAAAAAAAAGA
1 AAAAAAAAAGA
6151 AAAAAAAAAGA
1 AAAAAAAAAGA
6162 AAAA
1 AAAA
6166 TTTATATGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:6468 original size:25 final size:23
Alignment explanation
Indices: 6440--6512 Score: 64
Period size: 25 Copynumber: 3.1 Consensus size: 23
6430 TTAGATAGAA
6440 TATTTAATATAATATTATA-TAAATT
1 TATTTAATA-AA-ATTA-AGTAAATT
6465 TATTT-A-AAAATTAAGTAAATT
1 TATTTAATAAAATTAAGTAAATT
6486 TATTTAATTTAAAA-TAAGTTAAATT
1 TATTTAA--TAAAATTAAG-TAAATT
6511 TA
1 TA
6513 AATTTTTTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
20 1 0.02
21 15 0.36
22 3 0.07
23 1 0.02
24 5 0.12
25 17 0.40
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (23 bp):
TATTTAATAAAATTAAGTAAATT
Found at i:6521 original size:25 final size:26
Alignment explanation
Indices: 6459--6521 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 26
6449 TAATATTATA
6459 TAAATTTATTTAAAAATTAAGTAAATT
1 TAAATTTATTT-AAAATTAAGTAAATT
6486 T--ATTTAATTTAAAA-TAAGTTAAATT
1 TAAATTT-ATTTAAAATTAAG-TAAATT
6511 TAAATTT-TTTA
1 TAAATTTATTTA
6522 TTAAGATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
24 4 0.12
25 19 0.59
26 4 0.12
27 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (26 bp):
TAAATTTATTTAAAATTAAGTAAATT
Found at i:6835 original size:2 final size:2
Alignment explanation
Indices: 6828--6867 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
6818 TATCTCCATG
6828 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6868 ATCGGTCACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7253 original size:10 final size:10
Alignment explanation
Indices: 7226--7280 Score: 56
Period size: 10 Copynumber: 5.5 Consensus size: 10
7216 CACTTAGCTC
7226 ATATTAATTT
1 ATATTAATTT
* *
7236 GTAATAATTT
1 ATATTAATTT
*
7246 ATATTAATTA
1 ATATTAATTT
* **
7256 ATATCAATAC
1 ATATTAATTT
7266 ATATTAATTT
1 ATATTAATTT
7276 ATATT
1 ATATT
7281 GATTGATATA
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
10 34 1.00
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (10 bp):
ATATTAATTT
Found at i:7969 original size:3 final size:3
Alignment explanation
Indices: 7961--7986 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
7951 CTGAAAAATC
7961 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
7987 AAACATTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:11943 original size:6 final size:7
Alignment explanation
Indices: 11918--11942 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
11908 ACTCAACTCA
11918 AAAAATT
1 AAAAATT
11925 AAAAATT
1 AAAAATT
11932 AAAAATT
1 AAAAATT
11939 AAAA
1 AAAA
11943 TGAAGAACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAAATT
Found at i:12087 original size:2 final size:2
Alignment explanation
Indices: 12080--12117 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
12070 AAGAAGGCAT
12080 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12118 CACATATGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13037 original size:40 final size:38
Alignment explanation
Indices: 12992--13074 Score: 112
Period size: 41 Copynumber: 2.1 Consensus size: 38
12982 TTAAATCAAT
* *
12992 TTTTTTATGTTTTATATTTATTATTTAATTATAAAATATAA
1 TTTTTTATATTTTATA-TTATTATTTAA-CAT-AAATATAA
*
13033 TTTTTTATATTTTTTATTATTATTTAACATAAATATAA
1 TTTTTTATATTTTATATTATTATTTAACATAAATATAA
13071 TTTT
1 TTTT
13075 AACATATATG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
38 12 0.31
39 2 0.05
40 11 0.28
41 14 0.36
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (38 bp):
TTTTTTATATTTTATATTATTATTTAACATAAATATAA
Found at i:13048 original size:43 final size:37
Alignment explanation
Indices: 12989--13074 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 37
12979 GTTTTAAATC
*
12989 AATTTTTTTATGTTTTATATTTATTATTTAATTATAAAATAT
1 AATTTTTTTA-GTTTT-TA-TTATTATTTAA-CAT-AAATAT
*
13031 AATTTTTTATATTTTTTATTATTATTTAACATAAATAT
1 AATTTTTT-TAGTTTTTATTATTATTTAACATAAATAT
13069 AATTTT
1 AATTTT
13075 AACATATATG
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
38 12 0.29
39 2 0.05
40 11 0.27
41 2 0.05
42 12 0.29
43 2 0.05
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (37 bp):
AATTTTTTTAGTTTTTATTATTATTTAACATAAATAT
Found at i:13520 original size:2 final size:2
Alignment explanation
Indices: 13513--13538 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13503 GCATGAGATA
13513 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
13539 TGCAAAACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16549 original size:9 final size:10
Alignment explanation
Indices: 16526--16550 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
16516 CGAAGTAGGT
16526 AAAAATAATG
1 AAAAATAATG
16536 AAAAATAATG
1 AAAAATAATG
16546 AAAAA
1 AAAAA
16551 GCTTATGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (10 bp):
AAAAATAATG
Found at i:17562 original size:38 final size:34
Alignment explanation
Indices: 17503--17572 Score: 95
Period size: 38 Copynumber: 1.9 Consensus size: 34
17493 AAATAATATT
*
17503 TTTAAAAAAATATAATTAATATATTATTTTTTAA
1 TTTAAAAAAATATAATTAATATATAATTTTTTAA
17537 TTTAAATAAAATAATACATTAAATATATAATTTTTT
1 TTTAAA-AAAAT-ATA-ATT-AATATATAATTTTTT
17573 TAAATAGTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 6 0.19
35 5 0.16
36 3 0.10
37 3 0.10
38 14 0.45
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (34 bp):
TTTAAAAAAATATAATTAATATATAATTTTTTAA
Found at i:18100 original size:32 final size:32
Alignment explanation
Indices: 18059--18132 Score: 123
Period size: 32 Copynumber: 2.3 Consensus size: 32
18049 TTTAAGATAT
18059 TTTAAAATAACATTTATT-TTAATATTATTAAA
1 TTTAAAATAACATTTATTCTTAATA-TATTAAA
*
18091 TTTAAAATAATATTTATTCTTAATATATTAAA
1 TTTAAAATAACATTTATTCTTAATATATTAAA
18123 TTTAAAATAA
1 TTTAAAATAA
18133 AAATGTTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
32 34 0.85
33 6 0.15
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (32 bp):
TTTAAAATAACATTTATTCTTAATATATTAAA
Found at i:18207 original size:3 final size:3
Alignment explanation
Indices: 18199--18232 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
18189 AAGATAAAAA
18199 ATT ATT ATT ATT A-T ATT ATT ATT A-T ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
18233 GTATTTATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 25 0.86
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:18216 original size:14 final size:14
Alignment explanation
Indices: 18199--18232 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
18189 AAGATAAAAA
18199 ATTATTATTAT-TAT
1 ATTATTATTATAT-T
18213 ATTATTATTATATT
1 ATTATTATTATATT
18227 ATTATT
1 ATTATT
18233 GTATTTATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 18 0.95
15 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
ATTATTATTATATT
Found at i:18217 original size:11 final size:11
Alignment explanation
Indices: 18201--18237 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
18191 GATAAAAAAT
18201 TATTATTATTA
1 TATTATTATTA
18212 TATTATTATTA
1 TATTATTATTA
*
18223 TATTATTATTG
1 TATTATTATTA
18234 TATT
1 TATT
18238 TATACCCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (11 bp):
TATTATTATTA
Found at i:18589 original size:21 final size:20
Alignment explanation
Indices: 18563--18605 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
18553 AATTATTTAA
18563 TTTAAATAAAAAT-TTAAATAT
1 TTTAAA-AAAAATATT-AATAT
*
18584 TTTAAAAATAATATTAATAT
1 TTTAAAAAAAATATTAATAT
18604 TT
1 TT
18606 AATAATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAAAAAAAATATTAATAT
Found at i:18938 original size:22 final size:23
Alignment explanation
Indices: 18897--18965 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 23
18887 TTATATAAAT
*
18897 ATATAAAATTTTTAACATAATTATA
1 ATATAAAA-TATTAA-ATAATTATA
*
18922 ATATAAAA-ATTAAATAAATATA
1 ATATAAAATATTAAATAATTATA
* *
18944 ATTTAAAATATATAAATTATTA
1 ATATAAAATAT-TAAATAATTA
18966 AAGTTACTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
22 15 0.41
23 6 0.16
24 8 0.22
25 8 0.22
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (23 bp):
ATATAAAATATTAAATAATTATA
Found at i:19263 original size:30 final size:31
Alignment explanation
Indices: 19222--19322 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 31
19212 ATAAATTAAA
19222 ATAT-AATATAAATATTTAATTTA-AAAA-T
1 ATATAAATATAAATATTTAATTTATAAAATT
19250 ATATAATATATAAAT-TATTAATTTATTAAAATTT
1 ATATAA-ATATAAATAT-TTAATTTA-TAAAA-TT
* *
19284 ATATAAATATAAAATATTTAA-ATATAATTATT
1 ATATAAATAT-AAATATTTAATTTATAA-AATT
19316 ATATAAA
1 ATATAAA
19323 AAATATAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 16
0.77 0.03 0.20
Matches are distributed among these distances:
28 4 0.07
29 2 0.03
30 16 0.26
32 16 0.26
33 7 0.11
34 15 0.25
35 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
ATATAAATATAAATATTTAATTTATAAAATT
Found at i:19307 original size:15 final size:15
Alignment explanation
Indices: 19226--19310 Score: 50
Period size: 15 Copynumber: 5.5 Consensus size: 15
19216 ATTAAAATAT
19226 AATAT-AAATATTT-
1 AATATAAAATATTTA
* *
19239 AATTTAAAAATATATA
1 AATAT-AAAATATTTA
*
19255 ATATATAAATTA-TTA
1 A-ATATAAAATATTTA
* *
19270 ATTTATTAAAATTTATATA
1 A-ATA-TAAAA--TATTTA
19289 AATATAAAATATTTA
1 AATATAAAATATTTA
19304 AATATAA
1 AATATAA
19311 TTATTATATA
Statistics
Matches: 54, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
13 4 0.07
15 25 0.46
16 10 0.19
17 8 0.15
18 4 0.07
19 3 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATATAAAATATTTA
Found at i:19348 original size:2 final size:2
Alignment explanation
Indices: 19341--19365 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19331 ATAAACATGC
19341 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
19366 AATTTGGCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19821 original size:22 final size:22
Alignment explanation
Indices: 19779--19822 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
19769 AGGTCGGATC
*
19779 AATTCAGATTTTTAAATTTTTA
1 AATTCAGATTTTTAAAGTTTTA
*
19801 AATTCAGATCTTTT-TAGTTTTA
1 AATTCAGAT-TTTTAAAGTTTTA
19823 CATCTTTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.55
Consensus pattern (22 bp):
AATTCAGATTTTTAAAGTTTTA
Found at i:20028 original size:16 final size:16
Alignment explanation
Indices: 20004--20034 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19994 TGTGTTAATT
20004 ATTTAGATCATTTTAA
1 ATTTAGATCATTTTAA
*
20020 ATTTTGATCATTTTA
1 ATTTAGATCATTTTA
20035 GACTTGATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (16 bp):
ATTTAGATCATTTTAA
Found at i:20130 original size:5 final size:5
Alignment explanation
Indices: 20120--20184 Score: 66
Period size: 5 Copynumber: 13.2 Consensus size: 5
20110 AAAAATTTTT
*
20120 AATTA AATTA AATTA AATTAA AATT- AATT- AATT- AATTA AATT- TATTA
1 AATTA AATTA AATTA AATT-A AATTA AATTA AATTA AATTA AATTA AATTA
20167 AATTAA AATTAA AATTA A
1 AATT-A AATT-A AATTA A
20185 TAAATATATA
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
4 15 0.28
5 23 0.43
6 16 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
AATTA
Found at i:20145 original size:6 final size:6
Alignment explanation
Indices: 20120--20184 Score: 50
Period size: 6 Copynumber: 11.0 Consensus size: 6
20110 AAAAATTTTT
*
20120 AATT-A AATT-A AATT-A AATTAA AATT-- AATTAA TTAATTAA ATTTATTA
1 AATTAA AATTAA AATTAA AATTAA AATTAA AATTAA --AATTAA AATTA--A
20167 AATTAA AATTAA AATTAA
1 AATTAA AATTAA AATTAA
20185 TAAATATATA
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
4 4 0.08
5 14 0.27
6 22 0.43
8 11 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (6 bp):
AATTAA
Found at i:20457 original size:7 final size:8
Alignment explanation
Indices: 20440--20464 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
20430 TCAAAATATT
20440 AAAAATAA
1 AAAAATAA
20448 AAAAATAA
1 AAAAATAA
20456 AAAAATAA
1 AAAAATAA
20464 A
1 A
20465 TTATCTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:20910 original size:11 final size:11
Alignment explanation
Indices: 20887--20928 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
20877 TAATTTTATT
20887 AATTAAA-TTA
1 AATTAAATTTA
**
20897 AATTTGATTTA
1 AATTAAATTTA
20908 AATTAAATTTA
1 AATTAAATTTA
*
20919 AATTACATTT
1 AATTAAATTT
20929 TTTTAATATC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
10 5 0.19
11 21 0.81
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (11 bp):
AATTAAATTTA
Found at i:21352 original size:2 final size:2
Alignment explanation
Indices: 21345--21370 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21335 CAGCCGTCAA
21345 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
21371 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:29909 original size:13 final size:14
Alignment explanation
Indices: 29891--29924 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
29881 AATTTTTTAA
29891 ATTTTTT-AAATAT
1 ATTTTTTAAAATAT
*
29904 ATTTTTTAAAATGT
1 ATTTTTTAAAATAT
29918 ATTTTTT
1 ATTTTTT
29925 TTTATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (14 bp):
ATTTTTTAAAATAT
Found at i:30526 original size:11 final size:11
Alignment explanation
Indices: 30510--30535 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
30500 TGTTATATTA
30510 TAAAATTAATT
1 TAAAATTAATT
30521 TAAAATTAATT
1 TAAAATTAATT
30532 TAAA
1 TAAA
30536 TTCATCGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TAAAATTAATT
Found at i:40695 original size:16 final size:17
Alignment explanation
Indices: 40656--40702 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
40646 ATATTAAATT
40656 AAATTATATATATAATA
1 AAATTATATATATAATA
* *
40673 AATATTAAATAT-TATTA
1 AA-ATTATATATATAATA
40690 AAATTATATATAT
1 AAATTATATATAT
40703 TGAATGATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 8 0.32
17 9 0.36
18 8 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATTATATATATAATA
Found at i:40697 original size:34 final size:36
Alignment explanation
Indices: 40643--40819 Score: 119
Period size: 38 Copynumber: 5.2 Consensus size: 36
40633 GTAATTATTA
*
40643 AAAATATTAAATT-AAATTATATATATAATAAAT-AT
1 AAAATA-TATATTAAAATTATATATATAATAAATAAT
* * *
40678 TAAATAT-TATTAAAATTATATATAT--TGAATGAT
1 AAAATATATATTAAAATTATATATATAATAAATAAT
* *
40711 AAAATATAAATTAAAA--ATATAT-TAATAATTAAT
1 AAAATATATATTAAAATTATATATATAATAAATAAT
* * *
40744 --TA-AT-TATT-AAATTATATTTATATTAAATAAT
1 AAAATATATATTAAAATTATATATATAATAAATAAT
* **
40775 AAAATATATAAATTAAAATTATATTTATTTTAAATAAT
1 AAAATATAT--ATTAAAATTATATATATAATAAATAAT
40813 AATAATA
1 AA-AATA
40820 ATTATTATTA
Statistics
Matches: 111, Mismatches: 15, Indels: 28
0.72 0.10 0.18
Matches are distributed among these distances:
28 3 0.03
29 3 0.03
30 7 0.06
31 11 0.10
32 10 0.09
33 17 0.15
34 23 0.21
35 6 0.05
37 3 0.03
38 24 0.22
39 4 0.04
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (36 bp):
AAAATATATATTAAAATTATATATATAATAAATAAT
Found at i:40703 original size:18 final size:18
Alignment explanation
Indices: 40646--40703 Score: 59
Period size: 17 Copynumber: 3.3 Consensus size: 18
40636 ATTATTAAAA
*
40646 ATATTAAATTAAATTATAT
1 ATATT-AATAAAATTATAT
40665 ATA-TAATAAATATTA-A-
1 ATATTAATAAA-ATTATAT
*
40681 ATATTATTAAAATTATAT
1 ATATTAATAAAATTATAT
40699 ATATT
1 ATATT
40704 GAATGATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
16 7 0.21
17 13 0.39
18 10 0.30
19 3 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATTAATAAAATTATAT
Found at i:40721 original size:62 final size:63
Alignment explanation
Indices: 40638--40833 Score: 161
Period size: 66 Copynumber: 3.1 Consensus size: 63
40628 TAAAAGTAAT
* *
40638 TATTAAA-AATATTAAAT-TAAATTATATATATAATAAAT-ATTAAAT-ATTATTAAAATTATA-
1 TATTAAATAATA--AAATATAAATTAAAAATAT-ATAAATAATTAAATAATTATT-AAATTATAT
40698 TA
62 TA
* * * *
40700 TATTGAATGATAAAATATAAATTAAAAATATATTAATAATTAATTAATTATTAAATTATATTTA
1 TATTAAATAATAAAATATAAATTAAAAATATATAAATAATTAAATAATTATTAAATTATA-TTA
* ** * * *
40764 TATTAAATAATAAAATATATAAATTAAAATTATATTTAT-TTTAAATAATAATAATAATTATTAT
1 TATTAAATAAT-AAA-ATATAAATTAAAAATATATAAATAATTAAATAATTATTA-AATTA-TAT
40828 TA
62 TA
40830 TATT
1 TATT
40834 TACATTAAAA
Statistics
Matches: 110, Mismatches: 14, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
61 9 0.08
62 32 0.29
63 9 0.08
64 11 0.10
65 14 0.13
66 33 0.30
67 2 0.02
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (63 bp):
TATTAAATAATAAAATATAAATTAAAAATATATAAATAATTAAATAATTATTAAATTATATTA
Found at i:40784 original size:66 final size:66
Alignment explanation
Indices: 40643--40799 Score: 173
Period size: 66 Copynumber: 2.4 Consensus size: 66
40633 GTAATTATTA
* *
40643 AAAATAT-TAAATTAAATTATATATATAATAAATATTAAATATTATTAAAATTATATATATTGAA
1 AAAATATATAAATTAAA-AATATAT-TAATAAATATT-AATATTATTAAAATTATATATATTAAA
*
40707 TGAT
63 TAAT
*
40711 -AAA-ATATAAATTAAAAATATATTAATAATTAATT-A-ATTATT-AAATTATATTTATATTAAA
1 AAAATATATAAATTAAAAATATATTAATAAAT-ATTAATATTATTAAAATTATA--TATATTAAA
40771 TAAT
63 TAAT
*
40775 AAAATATATAAATTAAAATTATATT
1 AAAATATATAAATTAAAAATATATT
40800 TATTTTAAAT
Statistics
Matches: 78, Mismatches: 5, Indels: 14
0.80 0.05 0.14
Matches are distributed among these distances:
62 8 0.10
63 6 0.08
64 12 0.15
65 10 0.13
66 30 0.38
67 12 0.15
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (66 bp):
AAAATATATAAATTAAAAATATATTAATAAATATTAATATTATTAAAATTATATATATTAAATAA
T
Found at i:40794 original size:38 final size:37
Alignment explanation
Indices: 40728--40858 Score: 116
Period size: 34 Copynumber: 3.7 Consensus size: 37
40718 AAATTAAAAA
* * *
40728 TATATT-AATAATTAATTAAT-TATT-AAATTATATT
1 TATATTAAATAATAAAATAATAAATTAAAATTATATT
40762 TATATTAAATAATAAAATATATAAATTAAAATTATATT
1 TATATTAAATAATAAAATA-ATAAATTAAAATTATATT
* **
40800 TATTTTAAATAAT--AATAAT-AATTATTATTATATT
1 TATATTAAATAATAAAATAATAAATTAAAATTATATT
*
40834 TACATT-AA-AATAAAAATAAATAAAT
1 TATATTAAATAAT-AAAAT-AATAAAT
40859 AATAATTTTA
Statistics
Matches: 80, Mismatches: 8, Indels: 15
0.78 0.08 0.15
Matches are distributed among these distances:
32 3 0.04
33 2 0.03
34 23 0.29
35 15 0.19
36 9 0.11
37 6 0.08
38 22 0.28
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (37 bp):
TATATTAAATAATAAAATAATAAATTAAAATTATATT
Found at i:40830 original size:34 final size:34
Alignment explanation
Indices: 40733--40852 Score: 114
Period size: 38 Copynumber: 3.3 Consensus size: 34
40723 AAAAATATAT
40733 TAATAATTAATTAATTATTAAATTATATTTATATTAAA
1 TAATAA-TAA-TAATTATT--ATTATATTTATATTAAA
** *
40771 TAATAAAATATATAAATTAAAATTATATTTATTTTAAA
1 TAAT--AATA-AT-AATTATTATTATATTTATATTAAA
*
40809 TAATAATAATAATTATTATTATATTTACATTAAAA
1 TAATAATAATAATTATTATTATATTTATATT-AAA
*
40844 TAAAAATAA
1 TAATAATAA
40853 ATAAATAATA
Statistics
Matches: 69, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
34 17 0.25
35 13 0.19
36 4 0.06
38 24 0.35
39 3 0.04
40 8 0.12
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (34 bp):
TAATAATAATAATTATTATTATATTTATATTAAA
Found at i:41912 original size:26 final size:28
Alignment explanation
Indices: 41874--41928 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 28
41864 ATGATAATTT
*
41874 TTTTATTTAAATTTCTTAAAATTTTTTA
1 TTTTATTTAAATTTCTTAAAACTTTTTA
*
41902 TTTT-TTT-AATTTTTTAAAACTTTTTA
1 TTTTATTTAAATTTCTTAAAACTTTTTA
41928 T
1 T
41929 AATTACATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 18 0.72
27 3 0.12
28 4 0.16
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTTATTTAAATTTCTTAAAACTTTTTA
Found at i:42016 original size:27 final size:27
Alignment explanation
Indices: 41984--42044 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
41974 ATATCATATT
41984 ATTATTTTTAATAAAATTAATAATTAA
1 ATTATTTTTAATAAAATTAATAATTAA
42011 ATTATTTTTAATAAAATTAATAATTAA
1 ATTATTTTTAATAAAATTAATAATTAA
42038 ATTATTT
1 ATTATTT
42045 AGTTAATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
ATTATTTTTAATAAAATTAATAATTAA
Found at i:42027 original size:15 final size:15
Alignment explanation
Indices: 41984--42029 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
41974 ATATCATATT
41984 ATTATTTTTAATAAA
1 ATTATTTTTAATAAA
* *
41999 ATTA---ATAATTAA
1 ATTATTTTTAATAAA
42011 ATTATTTTTAATAAA
1 ATTATTTTTAATAAA
42026 ATTA
1 ATTA
42030 ATAATTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
12 10 0.42
15 14 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATTTTTAATAAA
Found at i:43444 original size:18 final size:18
Alignment explanation
Indices: 43408--43463 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
43398 CCTATTAAAT
*
43408 TTTATTTAAAATATTATA
1 TTTATATAAAATATTATA
43426 TTTATATAAAAT-TTA-A
1 TTTATATAAAATATTATA
43442 --TATATAATAAT-TTATA
1 TTTATATAA-AATATTATA
43458 -TTATAT
1 TTTATAT
43464 TAATGAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 7 0.21
15 6 0.18
16 2 0.06
17 8 0.24
18 11 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTATATAAAATATTATA
Found at i:43653 original size:18 final size:18
Alignment explanation
Indices: 43626--43680 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
43616 TTATATCAAC
43626 ATAATATTTTATTATAATT
1 ATAAT-TTTTATTATAATT
* *
43645 ATAATTTTT-TACATAATA
1 ATAATTTTTAT-TATAATT
*
43663 ATAATTTTTAATATAATT
1 ATAATTTTTATTATAATT
43681 TATATTATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
17 1 0.03
18 23 0.79
19 5 0.17
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
ATAATTTTTATTATAATT
Found at i:43986 original size:29 final size:30
Alignment explanation
Indices: 43932--43992 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
43922 AATTATATTA
43932 TATTTAAATATTTTATTAAATGAT-AATTT
1 TATTTAAATATTTTATTAAATGATAAATTT
*
43961 TATTTAAAATATTTTAATT-TAT-ATAAATTT
1 TATTT-AAATATTTT-ATTAAATGATAAATTT
43991 TA
1 TA
43993 ATATAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 7 0.25
30 18 0.64
31 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (30 bp):
TATTTAAATATTTTATTAAATGATAAATTT
Done.